The long line of people walking purposefully through the darkness this morning stretched as far as our car's headlights could illuminate.

It was 5.30am and still an hour before sunrise but much of East Timor had been up for hours preparing for its first ever fully free and fair election.

"We're all heading to the polling station," said Alberto da Costa, who was accompanied by his wife and children. "We've been walking since 3am but this is the best time of day to vote because it is not yet too hot."

By the time the polling stations opened an hour and a half later the queues in some places were several hundred people long. But as the sun rose higher and higher the people's determination showed no sign of flagging despite the sweltering heat.

"We'll wait as long as it takes," said Maria, as she waited in line in Manututo, about 30 miles east of the capital, Dili, after a comparatively brief two-mile walk. "This is going to decide the future of East Timor."

People's enthusiasm was so great that in some places the polls were able to close by early afternoon as everyone on the roll had voted.

Nine hours later, when the polls were meant to close, thousands of people were still waiting in line as local officials struggled to find people's names in the Tolstoyesque electoral registers. The election regulations state that anyone queuing by 4pm will be allowed to cast their ballot.

A few minor incidents were reported, but for the most part everything went smoothly.

The East Timorese are voting for an 88-member assembly that will write the constitution and prepare for full independence, expected to be some time next year.

Fretilin (the Independent Revolutionary Front of East Timor), which mounted the first drive for independence after the Portuguese colonisers withdrew in 1974, is expected to win a majority but no one knows how large it will be.

The election is being held exactly two years after the East Timorese voted overwhelmingly to secede from Indonesia following 24 years of repressive occupation during which time an estimated 200,000 people were killed or died of starvation.

The Indonesian military and its local militias responded to the result of that ballot by killing hundreds more people, destroying more than three-quarters of the buildings in the former Portuguese colony and forcibly relocating more than 250,000 people to Indonesian West Timor.

International troops and a UN transitional administration have steadily built the nation (not "rebuilding", because there was nothing left to rebuild) and are in the process of handing over authority to the East Timorese.

Nation-building in East Timor is much more than bricks and mortar. There are still more than 80,000 people stuck in West Timor and until a reconciliation process with the militias is established the people will find it very hard to move on.

Earlier this week, members of the steering committee of the proposed independent reception, truth and reconciliation commission unveiled their plans for a scheme that could well become a blueprint for post-conflict situations around the world.

The commission, which will inquire into human rights violations on all sides between April 1974, when Portugal withdrew from its former colony, to October 1999, aims to seek the truth, facilitate the return and reconciliation of the refugees still in West Timor, and make recommendations for future action.

It is expected that that perpetrators of minor offences, many of whom were forced to join the militias, will be tried by traditional chiefs, given community service sentences and then complete the reconciliation process. Those suspected of serious crimes will have to face formal prosecution.

"Yes we want reconciliation but we also need justice," said Aniceto Guterres, one member of the committee. "There cannot be amnesties and reconciliation without justice for all the people that suffered so much."

Forty-eight women living in the border town of Maliana who lost their husbands during the orgy of violence in 1999 are a typical example. They have set up a cooperative to make money but are clearly still angry and traumatised.

"I know who killed my husband and I'm ready to testify at his trial," said Augusta da Silva, 30, who works in the cooperative's shop. "What's important is that all the killers are tried first. Once that's happened there'll be no hard feelings in my heart."